Ic@sUdZddlTddlZddlmZddlmZddlmZddlmZddlmZddl Td Z d Z d Z d fd YZ dfdYZdfdYZdfdYZdefdYZdefdYZdfdYZdefdYZdefdYZedZdS(s This module provides code to work with the sprotXX.dat file from Utilities for working with FASTA-formatted sequences (OBSOLETE). http://www.expasy.ch/sprot/sprot-top.html Please see Bio.SwissProt for alternatives for the functionality in this module. Tested with: Release 37, Release 38, Release 39 Limited testing with: Release 51, 54 Classes: Record Holds SwissProt data. Reference Holds reference data from a SwissProt entry. Iterator Iterates over entries in a SwissProt file. Dictionary Accesses a SwissProt file using a dictionary interface. RecordParser Parses a SwissProt record into a Record object. SequenceParser Parses a SwissProt record into a SeqRecord object. _Scanner Scans SwissProt-formatted data. _RecordConsumer Consumes SwissProt data to a SProt.Record object. _SequenceConsumer Consumes SwissProt data to a SeqRecord object. Functions: index_file Index a SwissProt file for a Dictionary. i(t*N(tFile(tIndex(tAlphabet(tSeq(t SeqRecordccsddlm}ddl}|}d}xT|D]L}||7}|d dkr2|j|}|j|}d}|Vq2q2WdS(Ni(t RecordParsertis//(tSProtRt cStringIOtStringIOtparse(thandleRR tparserttexttlinetrecord((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR 0s    cCsddlm}|}y|j|}Wn:tk rh}|jjdr_tdqi|nX|j}|rtdn|S(Ni(RsLine does not start with 'ID':sNo SwissProt record founds$More than one SwissProt record found(RRR t ValueErrortmessaget startswithtread(R RR Rterrort remainder((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR=s   s .,;tRecordcBseZdZdZRS(sHolds information from a SwissProt record. Members: entry_name Name of this entry, e.g. RL1_ECOLI. data_class Either 'STANDARD' or 'PRELIMINARY'. molecule_type Type of molecule, 'PRT', sequence_length Number of residues. accessions List of the accession numbers, e.g. ['P00321'] created A tuple of (date, release). sequence_update A tuple of (date, release). annotation_update A tuple of (date, release). description Free-format description. gene_name Gene name. See userman.txt for description. organism The source of the sequence. organelle The origin of the sequence. organism_classification The taxonomy classification. List of strings. (http://www.ncbi.nlm.nih.gov/Taxonomy/) taxonomy_id A list of NCBI taxonomy id's. host_organism A list of NCBI taxonomy id's of the hosts of a virus, if any. references List of Reference objects. comments List of strings. cross_references List of tuples (db, id1[, id2][, id3]). See the docs. keywords List of the keywords. features List of tuples (key name, from, to, description). from and to can be either integers for the residue numbers, '<', '>', or '?' seqinfo tuple of (length, molecular weight, CRC32 value) sequence The sequence. cCsd|_d|_d|_d|_g|_d|_d|_d|_d|_ d|_ d|_ d|_ g|_ g|_g|_g|_g|_g|_g|_g|_d|_d|_dS(NR(tNonet entry_namet data_classt molecule_typetsequence_lengtht accessionstcreatedtsequence_updatetannotation_updatet descriptiont gene_nametorganismt organelletorganism_classificationt taxonomy_idt host_organismt referencestcommentstcross_referencestkeywordstfeaturestseqinfotsequence(tself((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyt__init__ss,                     (t__name__t __module__t__doc__R0(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRPs"t ReferencecBseZdZdZRS(sHolds information from 1 references in a SwissProt entry. 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Members: data Record with SwissProt data. cCs d|_dS(N(RRI(R/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR0scCsdS(Ns%Bio.SwissProt.SProt._RecordConsumer()((R/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyt__repr__scCst|_g|_dS(N(RRIt_sequence_lines(R/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRps cCs,|j|jdj|j|j_dS(NR(t _clean_recordRIRFRR.(R/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRuscCsa|j}t|dkry|d|j_|djt|j_|djt|j_t|d|j_ npt|dkr|d|j_|djt|j_d|j_t|d|j_ nt d||jjdkrt d |jj|fn|jjdk r]|jjdkr]t d|jj|fndS(Niiiiiis!ID line has unrecognised format: tSTANDARDt PRELIMINARYtIPItReviewedt Unrevieweds%Unrecognized data class %s in line %stPRTs(Unrecognized molecule type %s in line %s(RRRRR( tsplitRTRIRtrstript_CHOMPRRtintRRR(R/Rtcols((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR s(    cCs_|djtjjd}x6|D].}|jr)|jjj|jq)q)WdS(Nit;(RRtstripRRIRRE(R/RRtac((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR0s"  c Cs|j}|jj}|jddks]|jddks]|jddkr|j}d}x<tt|D](}||jddkr|}qqW|dkstd||d}||jt}|d krd} n*|jd dkr|} n t|} |jddkrT|d| f|j _ q|jddkr|d| f|j _ q|jddkr|d| f|j _ qt std n|jd dks|jd dks|jddkryt|d} Wntk r1d} nX|jddkr`|d| f|j _ q|jd dkr|d| f|j _ q|jddkr|d| f|j _ qt std ntd|dS(NtCREATEDisLAST SEQUENCE UPDATEsLAST ANNOTATION UPDATEisREL.s"Could not find Rel. in DT line: %siRt.sShouldn't reach this line!sINTEGRATED INTOsSEQUENCE VERSIONs ENTRY VERSIONt INTEGRATEDs#I don't understand the date line %s(tupperRRtfindtrangeRTtAssertionErrorRRRIRRR tFalseR( R/RtuprlineRtuprcolst rel_indextindext version_indext str_versiontversion((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR7sR           cCs|jj|d7_dS(Ni(RIR!(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR!scCs|jj|d7_dS(Ni(RIR"(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR"scCs|jj|d7_dS(Ni(RIR#(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCs|jj|d7_dS(Ni(RIR$(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR$scCsP|djt}|jd}x'|D]}|jjj|jq)WdS(NiR(RRRRIR%REtlstrip(R/RRtcol((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR%s cCs|djt}|jd}|dkrn|| }|dksTtd|||djd}n|jd}|jjjg|D]}|j^qdS(Nit=it NCBI_TaxIDsUnexpected taxonomy type %sit,( RRRRRRIR&textendR(R/RRtdescrtidstid((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR&s   cCs|djt}|jd}|dkrn|| }|dksTtd|||djd}n|jd}|jjjg|D]}|j^qdS(NiRiRsUnexpected taxonomy type %siR( RRRRRRIR'RR(R/RRRRR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRs  cCsv|dj}|ddkr0|ddks@td|t}t|dd!|_|jjj|dS(Niit[it]sMissing brackets %si(RRR4RR5RIR(RE(R/Rtrntref((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRs 0 cCs@|jjstd|jjdjj|djdS(NsRP: missing RNii(RIR(RR6RER(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCs|jjstd|djjd}|jjd}x^|D]V}|sZqHn|jd}|| ||d}}|jj|j|fqHWdS(NsRC: missing RNiRiRi( RIR(RRRRR)RER(R/RRRRRttokenR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRs c Cs|jjstd|jd}|dkr@|| }n|jddkr8|djd}g|D]}|j^qo}g|D]}|r|^q}x|D]}|jd}t|dkstd||djt|d jt}}|jjdj}|j ||fqWnh|j}t|d ksftd||jjdjj |d jt|djtfdS( NsRX: missing RNs[NCBI, ExPASy, Israel, Japan]iRiis; sI don't understand RX line %sii( RIR(RRRRRTRRRE( R/RtindRtxRRWtvalueR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRs$    "' "cCs?|jjstd|jjd}|j|d7_dS(NsRA: missing RNii(RIR(RR7(R/RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCs?|jjstd|jjd}|j|d7_dS(NsRT: missing RNii(RIR(RR8(R/RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCs?|jjstd|jjd}|j|d7_dS(NsRL: missing RNii(RIR(RR9(R/RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCs|dd!dkr-|jjj|dn|dd!dkr|jjsf|jjj|dq|jjdc|d7 PCRATGWSPFRRSSPC LPTH' We want to check for this case and correct it as it happens. s -> iiiRs (it (RRTRtreplace(R/R!t descr_colst first_seqt second_seqt extra_infotextra_info_pos((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRes     cCsdS(N((R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCs_|j}t|dks.td|t|dt|d|df|j_dS(NisI don't understand SQ line %siii(RRTRRRIR-(R/RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRs "cCs&|jj|jddjdS(NRR(RRERR(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCsdS(N((R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCsmddddg}x3|D]+}t||}t|||jqWx|jD]}|j|qRWdS(NR!R"R#R$(RZtsetattrRR(t_clean_references(R/trectmemberstmtattrR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRs  cCsIdddg}x3|D]+}t||}t|||jqWdS(NR7R8R9(RZRR(R/RR R R ((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR s (#R1R2R3R0RRpRuRRRR!R"RR$R%R&RRRRRRRRRRRRRRRRRRR (((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRbsB     &  [          '             RfcBseZdZejdZdZdZdZdZ dZ dZ dZ d Z d Zd Zd Zd ZdZdZdZdZdZdZdZdZdZdZRS(sConsumer that converts a SwissProt record to a SeqRecord object. Members: data Record with SwissProt data. alphabet The alphabet the generated Seq objects will have. cCsd|_||_dS(sInitialize a Sequence Consumer Arguments: o alphabet - The alphabet to use for the generated Seq objects. If not supplied this will default to the generic protein alphabet. N(RRIRg(R/Rg((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyR0s cCsUtjd|j}tj||_d|j_d|j_d|_g|_dS(NR( RRgRRIR!R[Rt _current_refR(R/tseq((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRps    cCsx|jdk r5|jjdj|jd|_n|jjj|j_tjdj|j |j |j_ dS(NR(R( RRRIt annotationsRER!RRRFRRgR(R/((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRus  cCs |j}|d|j_dS(Ni(RRIR[(R/RR((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRs cCs|djjd}g|D]}|jr |j^q }y|jjdj|Wn!tk r||jjd|jdk std|jj|djd7_dS(sRA line, reference author(s).sRA: missing RNis N(RRRR7R(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCs>|jdk std|jj|djd7_dS(sRT line, reference title.sRT: missing RNis N(RRRR8R(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCs>|jdk std|jj|djd7_dS(s=RL line, reference 'location' - journal, volume, pages, year.sRL: missing RNis N(RRRtjournalR(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRscCs>|jdk std|jj|djd7_dS(sRC line, reference comment.sRC: missing RNis N(RRRRR(R/R((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRs(R1R2R3RRhR0RpRuRRR!RR"RRRRRRR%R&RRRRRRR(((s/oak/stanford/groups/akundaje/marinovg/programs/biopython-1.50.tar.gz/biopython-1.50/build/lib.linux-x86_64-2.7/Bio/SwissProt/SProt.pyRfs0             0   c Csddlm}tjj|s5td|ntj|dd}||tj$s.    >3)